Potential Energy Hypersurface Research Articles

Investigations on the E/Z-isomerism of neonicotinoids

We investigate the minimum-energy path for the rotation of formal C=N double bonds in molecules with guanidine-like substructures as present in the chemical class of neonicotinoids. The transitions between the E- and Z-isomers of several neonicotinoids using scans of the torsional potential energy hypersurfaces are quantified at the DFT-level of theory. The validity of using this ansatz is checked by single-point CCSD(T) calculations for model systems like nitroguanidine. A combined approach of theory and experiment permits to unambiguously identify the relevant isomers present at ambient conditions. As an example, MP2-GIAO predictions of the NMR spectra of E- and Z-Clothianidin are experimentally confirmed by low-temperature NMR-experiments identifying for the first time the hitherto unknown Z-Isomer of Clothianidin.

Probing multiphoton light-induced molecular potentials

The strong coupling between intense laser fields and valence electrons in molecules causes distortions of the potential energy hypersurfaces which determine the motion of the nuclei and influence possible reaction pathways. The coupling strength varies with the angle between the light electric field and valence orbital, and thereby adds another dimension to the effective molecular potential energy surface, leading to the emergence of light-induced conical intersections. Here, we demonstrate that multiphoton couplings can give rise to complex light-induced potential energy surfaces that govern molecular behavior. In the laser-induced dissociation of H2+, the simplest of molecules, we measure a strongly modulated angular distribution of protons which has escaped prior observation. Using two-color Floquet theory, we show that the modulations result from ultrafast dynamics on light-induced molecular potentials. These potentials are shaped by the amplitude, duration and phase of the dressing fields, allowing for manipulating the dissociation dynamics of small molecules.

Conformational diversity of the quercetin molecule: a quantum-chemical view

This paper focuses on the comprehensive conformational analysis of the quercetin molecule with a broad range of the therapeutic and biological actions. All possible conformers of these molecule, corresponding to the local minima on the potential energy hypersurface, have been obtained by the sequential rotation of its five hydroxyl groups and also by the rotation of its (A + C) and B rings relatively each other. Altogether, it was established 48 stable conformers, among which 24 conformers possess planar structure and 24 conformers – nonplanar structure. Their structural, symmetrical, energetical and polar characteristics have been investigated in details. Quantum-mechanical calculations indicate that conformers of the quercetin molecule are polar structures with a dipole moment, which varies within the range from 0.35 to 9.87 Debay for different conformers. Relative Gibbs free energies of these conformers are located within the range from 0.0 to 25.3 kcal·mol−1 in vacuum under normal conditions. Impact of the continuum with ε = 4 leads to the decreasing of the Gibbs free energies (–0.19–18.15 kcal·mol−1) and increasing of the dipole moment (0.57–12.48 D). It was shown that conformers of the quercetin molecule differ from each other by the intramolecular specific contacts (two or three), stabilizing all possible conformers of the molecule – H-bonds (both classical ОН…О and so-called unusual С′Н…О and ОН…С′) and attractive van-der-Waals contacts О…О. Obtained conformational analysis for the quercetin molecule enables to provide deeper understanding of the ‘structure-function’ relationship and also to suggest its mechanisms of the therapeutic and biological actions. Communicated by Ramaswamy H. Sarma

Photophysics of Emissive tzC[Isothiazolo‐Cytidine] and tzU[Isothiazolo‐Uridine] Pyrimidine Analogues

AbstractThe tzC and tzU emissive properties were investigated with the MS‐CASPT2 method and CASSCF/CASPT2 protocol, with inclusion of solvent effects with the aid of the PCM and Sequential QM/MM, the Free Energy Gradient methods. Theoretical vertical emission energies and Stokes shifts, using the ASEC‐FEG method, are in a good agreement with the experimental data, within the expected accuracy of CASPT2 method. Their emissive properties can be understood in analogy to the photophysical behaviour of the canonical uracil and cytosine pyrimidine nucleobases, for which the twisting of the C5C6 bond is the key for understanding their ultrashort radiationless decay times. For both tzC and tzU, the computed photophysical deactivation pathway, shows that the bright state goes directly to a minimum structure on its potential energy hypersurface , from where no conical intersection with the ground state can be reached, due to the steric hindrance of the C5C6 position, which forms the bridge between the rings in both molecules. Solvent effects place the conical intersection in higher energy region, reinforcing their emissive nature.

A Spectroscopic and Computationally Minimal Approach to the Analysis of Charge-Transfer Processes in Conformationally Fluxional Mixed-Valence and Heterobimetallic Complexes.

Class II mixed-valence bimetallic complexes {[Cp'(PP)M]C≡C-C≡N[M'(PP)'Cp']}2+ (M, M'=Ru, Fe; PP=dppe, (PPh3 )2 ; Cp'=Cp*, Cp) exist as conformational ensembles in fluid solution, with a population of structures ranging from cis- to trans-like geometries. Each conformer gives rise to its own series of low-energy intervalence charge-transfer (IVCT) and local d-d transitions, which overlap in the NIR region, giving complex band envelopes in the NIR absorption spectrum, which prevent any meaningful attempt at analysis of the band shape. However, DFT and time-dependent (TD)DFT calculations with dispersion-corrected global-hybrid (BLYP35-D3) or local hybrid (lh-SsirPW92-D3) functionals on a small number of optimised structures chosen to sample the ground state potential energy hypersurfaces of each of these complexes has proven sufficient to explain the major features of the electronic spectra. Although modest in terms of computational expense, this approach provides a more accurate description of the underlying molecular electronic structure than would be possible through analysis of the IVCT band by using the static point-charge model of Marcus-Hush theory and derivatives, or TDDFT calculations from a single (global) minimum energy geometry.

Photochemical Relaxation Pathways of 9 H-8-Azaguanine and 8 H-8-Azaguanine.

The photochemical reaction path approach, the MS-CASPT2 quantum-chemical method, and double-ζ basis sets (cc-pVDZ) were used to study 9 H-8-azaguanine and 8 H-8-azaguanine relaxation pathways. Several potential energy hypersurfaces were characterized by means of equilibrium geometries, surface crossings (conical intersections and singlet-triplet intersystem crossings), minimum energy paths, and linear interpolation in internal coordinates. The 9 H-8-azaguanine main photochemical event begins with the direct population of the 1(ππ* La) state, which evolves toward a conical intersection with the ground state after surmounting a small energy barrier, explaining why it is nonfluorescent. For 8 H-8-azaguanine, two relaxation mechanisms are possible, depending on the excitation energy. If the S1 1(ππ*) state is initially populated (lower-energy region), the system evolves barrierless to the S1 1(ππ*)min region, from where the excess energy is released. If the 1(ππ* La) state is populated (higher-energy radiation), the system will encounter conical intersections with the S2 1(nOπ*) and S1 1(ππ*) states before evolving to the 1(ππ* La)min region, from where a conical intersection with the ground state is accessible, favoring radiationless deactivation to the ground state. However, because a fraction of the population can be transferred from 1(ππ* La) to the S1 1(ππ*) state, emission from the S1 1(ππ*)min region is also expected, although weaker than it would be if the S1 1(ππ*) state were populated directly. Irrespective of the excitation energy, the emissive state is the same and a single fluorescence band is observed, with the strongest emission occurring upon excitation in the lower-energy region, as observed experimentally. Therefore, our computational study corroborates experimental results, attributing the emission of the neutral form of 8-azaguanine in solution to the presence of the minor 8 H-8-azaguanine tautomer, while the 9 H-8-azaguanine major tautomer is nonfluorescent.

Controlling tunneling in ammonia isotopomers.

We report results of full-dimensional variational rovibrational quantum-dynamical computations for several ammonia isotopomers, based on selected potential energy and electric dipole moment hypersurfaces. The variational rovibrational eigenstates have been used as a basis for the solution of the time-dependent Schrödinger equation for nuclear motion including coherent infrared multiphoton excitation. The theoretical and computational framework developed during this study enables the investigation of the coherent inhibition or enhancement of tunneling in ammonia isotopomers by appropriately chosen laser fields. Our quantum-dynamical computations include all vibrational and rotational degrees of freedom and assume neither the alignment nor the orientation of the molecules under investigation. Specific results include accurate rotational-vibrational levels for NH2D, NHD2, NHDMu, and NHDT, probability densities for structural parameters as a function of time from the full-dimensional wavepacket results, time-dependent chirality for the isotopically chiral molecule NHDT, and detailed analyses of the enhancement and inhibition of stereomutation dynamics.

Rovibrational quantum dynamics of the vinyl radical and its deuterated isotopologues.

Rotational-vibrational states up to 3200 cm-1, beyond the highest-lying stretching fundamental, are computed variationally for the vinyl radical (VR), H2Cβ[double bond, length as m-dash]CαH, and the following deuterated isotopologues of VR: CH2[double bond, length as m-dash]CD, CHD[double bond, length as m-dash]CH, and CD2[double bond, length as m-dash]CD. The height of the CαH tunneling rocking barrier of VR, partially responsible for the complex nuclear dynamics of VR and its isotopologues, is determined to be 1641 ± 25 cm-1 by the focal-point analysis approach. The definitive nuclear-motion computations performed utilize two previously published potential energy hypersurfaces and reveal interesting energy-level and tunneling patterns characterizing the internal motions of the four isotopologues. A full assignment, including symmetry labels, of the vibrational states computed for CH2[double bond, length as m-dash]CH is provided, whenever feasible, based on the analysis of wave functions and the related one- and two-mode reduced density matrices. The computed vibrational states of CH2[double bond, length as m-dash]CD and CD2[double bond, length as m-dash]CD are characterized up to slightly above the top of the barrier. Interestingly, it is the interplay of the ν6 (formally CH2 rock) and ν7 (formally CH rock) modes that determines the tunneling dynamics; thus, the description of tunneling in VR needs, as a minimum, the consideration of two in-plane bending motions at the two ends of the molecule. When feasible, the computed results are compared to their experimental counterparts as well as to previous computational results. Corrections to the placement of the ν4 and ν6 fundamentals of VR are proposed. Tunneling switching, a unique phenomenon characterizing tunneling in slightly asymmetric effective double-well potentials, is observed and discussed for CHD[double bond, length as m-dash]CH. Despite the extensive tunneling dynamics, the rotational energy-level structure of VR exhibits rigid-rotor-type behavior.

A prelude to building mathematical models for polypeptide folding: analysis on the conformational potential energy hypersurface cross-sections of N-acetyl-glycyl-glycine-N′-methylamide

Finding a relationship on how a three-dimensional protein folds from its linear amino acid chain gets more complex with increasing chain length, so working on a smaller peptide conformational problem can provide initial ideas on what are the main molecular forces and how these influence the folding process. Following the study of conformations of amino acid units entering the proteins to understand the secondary structure of small peptides, this paper proposes mathematical models for the several two-rotor cross-sections of the five-dimensional N-acetyl-glycyl-glycine-N′-methylamide potential energy hypersurface (PEHS). These cross-sections are extracted along the first glycine subunit, with its coordinates fixed at the five energy minima of the glycine diamide. The resulting mathematical models yield an average RMSE of 1.36 kJ mol−1 and an average R2 of 0.9923 with respect to energy values obtained from DFT calculations. The minima geometries obtained from these models are also in good agreement with DFT-optimized energy minima conformers. An important aspect of this study also tackles the relationship between the PEHS of the glycyl-glycine diamide and its glycine subunits. It has been observed that there are deviations up to 28.35 kJ mol−1 and 29.52 kJ mol−1 between the PEHS cross-sections along γL and γD conformations, respectively, in the first glycine subunit. This may suggest that there are significant backbone–backbone intermolecular forces acting on the dipeptide. The abovementioned findings can help in developing more complex mathematical models for polypeptide folding from amino acid subunits.

Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes.

For a theoretical understanding of the reactivity of complex chemical systems, relative energies of stationary points on potential energy hypersurfaces need to be calculated to high accuracy. Due to the large number of intermediates present in all but the simplest chemical processes, approximate quantum chemical methods are required that allow for fast evaluations of the relative energies but at the expense of accuracy. Despite the plethora of benchmark studies, the accuracy of a quantum chemical method is often difficult to assess. Moreover, a significant improvement of a method's accuracy (e.g., through reparameterization or systematic model extension) is rarely possible. Here, we present a new approach that allows for the systematic, problem-oriented, and rolling improvement of quantum chemical results through the application of Gaussian processes. Due to its Bayesian nature, reliable error estimates are provided for each prediction. A reference method of high accuracy can be employed if the uncertainty associated with a particular calculation is above a given threshold. The new data point is then added to a growing data set in order to continuously improve the model and, as a result, all subsequent predictions. Previous predictions are validated by the updated model to ensure that uncertainties remain within the given confidence bound, which we call backtracking. We demonstrate our approach with the example of a complex chemical reaction network.

The Light-Driven Isomerization of Aqueous Nitrate: A Theoretical Perspective

The front cover artwork is provided by the CTCP group at Massey University. The image shows the potential energy hypersurface for the NO3− to ONOO− rearrangement. The water and shining light symbolize the photochemical process in aqueous solution. Read the full text of the Article at10.1002/cptc.201800022.

A genetic algorithm survey on closed-shell atomic nitrogen clusters employing a quantum chemical approach.

The DFT potential energy hypersurfaces of closed-shell nitrogen clusters up to ten atoms are explored via a genetic algorithm (GA). An atom-atom distance threshold parameter, controlled by the user, and an "operator manager" were added to the standard evolutionary procedure. Both B3LYP and PBE exchange-correlation functionals with 6-31G basis set were explored using the GA. Further evaluation of the structures generated were performed through reoptimization and vibrational analysis within MP2 and CCSD(T) levels employing larger correlation consistent basis set. The binding energies of all stable structures found are calculated and compared, as well as their energies relative to the dissociation into N2, [Formula: see text] and [Formula: see text] molecules. With the present approach, we confirmed some previously reported polynitrogen structures and predicted the stability of new ones. We can also conclude that the energy surface profile clearly depends on the calculation method employed.

Computational Spectroscopic Characterization of a Bistable Binuclear Complex [(CO)2(benzoate)FeII/III(terephthalate)CoIII/II(benzoate)(CO)2

Electric dipole moments, polarizabilities, and IR, Raman, optical rotatory dispersion, and electronic and vibrational circular dichroism spectra of the four cis–trans isomers of the proposed [(CO)2(benzoate)FeII/III(terephthalate)CoIII/II(benzoate)(CO)2]+ binuclear complex, having bistablity due to intramolecular charge transfer (IMCT), is investigated using the time-dependent density functional theory ((TD)DFT) B3LYP/6–31G(d,p)[LanL2DZ] method. Results show that the two FeII–CoIII and FeIII–CoII IMCT states of this binuclear complex have distinctly different spectroscopic, optical, and electric response properties, and are sensitive to the cis–trans arrangement of the ligands around the two metallic centres. Furthermore, intrinsic reaction coordinates inter-connecting the two IMCT states are identified using the Duschinsky matrix method. Only one or two of the normal coordinates remain almost (above 80 %) intact during the IMCT reaction which denotes global changes in the bonding strengths and potential energy hypersurface of this bistable binuclear complex. Analysis of the calculated spin densities characterizes the IMCT transition state structures of the trans–trans, cis–cis, and trans–cis isomers as early, early, and late transition states, respectively.

Predicting the structures and associated phase transition mechanisms in disordered crystals via a combination of experimental and theoretical methods.

Disordered materials make up a large proportion of condensed phase systems, but the difficulties in describing their structures and molecular dynamics limit their potential applications. Disordered crystalline systems, also known as plastic crystals, offer a unique perspective into these factors because the systems retain a degree of crystallinity, reducing the degrees of freedom that must be explored when interpreting the results. However, while disordered crystals do diffract X-rays, it is difficult to fully resolve meaningful crystalline structures, with the best scenario resulting in lattice parameters. In this study, we use a combination of experimental terahertz time-domain spectroscopy, and theoretical solid-state ab initio density functional theory and molecular dynamics simulations to fully elucidate the structures and associated dynamics of organic molecular solids. The results highlight that this combination provides a complete description of the energetic and mechanistic pathways involved in the formation of disordered crystals, and highlights the importance of low-frequency dynamics in their properties. Finally, with structures fully determined and validated by the experimental results, recent progress into anharmonic calculations, namely the quasi-harmonic approximation method, enables full temperature and pressure-dependent properties to be understood within the framework of the potential energy hyper-surface structure.

Effects of collision energy and vibrational excitation of CH3+ cations on its reactivity with hydrocarbons: But-2-yne CH3CCCH3 as reagent partner.

The methyl carbocation is ubiquitous in gaseous environments, such as planetary ionospheres, cometary comae, and the interstellar medium, as well as combustion systems and plasma setups for technological applications. Here we report on a joint experimental and theoretical study on the mechanism of the reaction CH3+ + CH3CCCH3 (but-2-yne, also known as dimethylacetylene), by combining guided ion beam mass spectrometry experiments with ab initio calculations of the potential energy hypersurface. Such a reaction is relevant in understanding the chemical evolution of Saturn's largest satellite, Titan. Two complementary setups have been used: in one case, methyl cations are generated via electron ionization, while in the other case, direct vacuum ultraviolet photoionization with synchrotron radiation of methyl radicals is used to study internal energy effects on the reactivity. Absolute reactive cross sections have been measured as a function of collision energy, and product branching ratios have been derived. The two most abundant products result from electron and hydride transfer, occurring via direct and barrierless mechanisms, while other channels are initiated by the electrophilic addition of the methyl cation to the triple bond of but-2-yne. Among the minor channels, special relevance is placed on the formation of C5H7+, stemming from H2 loss from the addition complex. This is the only observed condensation product with the formation of new C-C bonds, and it might represent a viable pathway for the synthesis of complex organic species in astronomical environments and laboratory plasmas.

A quantum dynamical study of the photoelectron spectra and the Renner-Teller effect in BrCN and ClCN based on four-component potential energy hypersurfaces

In this work we investigate the Renner-Teller effect (RTE) in the photoelectron spectra of ClCN and BrCN. The spectra were calculated by a nuclear wave packet propagation on coupled cationic Π1/2/Π3/2 surfaces obtained by the four-component Fock-space coupled cluster method. The scalar relativistic, spin-orbit and electron correlation effects are consistently included in the hypersurfaces for the three internal nuclear degrees of freedom. In contrast to other approaches no coupling matrix elements involving the spin-orbit operator together with an explicit representation of the wave function were necessary. The current study extends earlier work on the RTE for the derivation of the Renner-Teller parameters c and d where only one nuclear degree of freedom was considered (Pernpointner and Salopiata, 2013). The outlined procedure is especially useful for electronic structure methods that yield accurate energies but do not provide an explicit wave function representation.

Strain-driven diffusion process during silicon oxidation investigated by coupling density functional theory and activation relaxation technique.

The reaction of oxygen molecules on an oxidized silicon model-substrate is investigated using an efficient potential energy hypersurface exploration that provides a rich picture of the associated energy landscape, energy barriers, and insertion mechanisms. Oxygen molecules are brought in, one by one, onto an oxidized silicon substrate, and accurate pathways for sublayer oxidation are identified through the coupling of density functional theory to the activation relaxation technique nouveau, an open-ended unbiased reaction pathway searching method, allowing full exploration of potential energy surface. We show that strain energy increases with O coverage, driving the kinetics of diffusion at the Si/SiO2 interface in the interfacial layer and deeper into the bulk: at low coverage, interface reconstruction dominates while at high coverage, oxygen diffusion at the interface or even deeper into the bottom layers is favored. A changing trend in energetics is observed that favors atomic diffusions to occur at high coverage while they appear to be unlikely at low coverage. Upon increasing coverage, strain is accumulated at the interface, allowing the oxygen atom to diffuse as the strain becomes large enough. The observed atomic diffusion at the interface releases the accumulated strain, which is consistent with a layer-by-layer oxidation growth.

A GRADIENT-CORRECTED HYBRID HF–DFT STUDY OF STRUCTURE AND VIBRATIONAL SPECTROSCOPIC PROPERTIES OF THE DICHLORODIOXOCHROMIUM(VI) COMPLEX WITH 1,10-PHENANTHROLINE

A b s t r a c t: In order to get a more exact basis for the band assignments in the case of dichlorodioxochromium(VI) complex with 1,10-phenanthroline (especially regarding the order of appearance of the antisymmetric and symmetric CrO2 stretching bands) a quantum chemical study of this system was carried out. Two levels of theory were employed – the HF/6-31++G(d,p) and the density-functional-theory-based (DFT) method B3–LYP/6- 31++G(d,p). Full geometry optimizations of the title complex were carried out, employing Schlegel's gradient optimization algorithm. Harmonic vibrational analyses of the stationary points located on both potential energy hypersurfaces were subsequently carried out in order to test their character and to compute the harmonic vibrational frequencies of the complex. Predictions of the ab initio and DFT quantum chemical approaches regarding the order of appearance of the antisymmetric and symmetric CrO2 stretching bands in the case of the studied complex were compared to the cases of analogous 2,2'-bipyridine and 2,2'-biquinoline complexes containing the CrO2 group, which were previously studied by us [1–6].

A multicomponent QM study of H2 dissociation on small aluminum cluster

H2 dissociation on small aluminum cluster, Al2, is studied using our multicomponent quantum-mechanical (MC_QM) method, which can take account of the nuclear quantum effect (NQE) of light nucleus, such as proton and deuteron. We demonstrate that no standard density functionals can reproduce CCSD(T) geometry of van der Waals Al2…H2 complex well, even though the empirical dispersion correction is included. Our MC_QM calculations reveal that NQE stabilizes Structures at each stationary point, and H2 dissociation reaction is the barrierless reaction on the MC_QM effective potential energy hypersurface. The H/D isotope effect on the dissociation reaction are also analyzed.

Ultrafast α -CC bond cleavage of acetone upon excitation to 3p and 3d Rydberg states by femtosecond time-resolved photoelectron imaging.

The radiationless electronic relaxation and α -CC bond fission dynamics of jet-cooled acetone in the S1 (nπ*) state and in high-lying 3p and 3d Rydberg states have been investigated by femtosecond time-resolved mass spectrometry and photoelectron imaging. The S1 state was accessed by absorption of a UV pump photon at selected wavelengths between λ = 320 and 250 nm. The observed acetone mass signals and the S1 photoelectron band decayed on sub-picosecond time scales, consistent with a recently proposed ultrafast structural relaxation of the molecules in the S1 state away from the Franck-Condon probe window. No direct signatures could be observed by the experiments for CC dissociation on the S1 potential energy hypersurface in up to 1 ns. The observed acetyl mass signals at all pump wavelengths turned out to be associated with absorption by the molecules of one or more additional pump and/or probe photons. In particular, absorption of a second UV pump photon by the S1 (nπ*) state was found to populate a series of high-lying states belonging to the n = 3 Rydberg manifold. The respective transitions are favored by much larger cross sections compared to the S1 ← S0 transition. The characteristic energies revealed by the photoelectron images allowed for assignments to the 3p and 3dyz states. At two-photon excitation energies higher than 8.1 eV, an ultrafast reaction pathway for breaking the α -CC bond in 50-90 fs via the 3dyz Rydberg state and the elusive ππ* state was observed, explaining the formation of acetyl radicals after femtosecond laser excitation of acetone at these wavelengths.